The detection of heart sounds using an acoustical sensor has been proposed for use in implantable medical device systems for use in detecting heart rhythms, verifying cardiac capture subsequent to a pacing pulse, and evaluating cardiac hemodynamics. Different and unique sounds are emitted from the heart during various points in the cardiac cycle which can be evaluated to monitor the heart rhythm as well as derive metrics of heart function. An acoustical sensor may be incorporated in an implantable medical device (IMD), such as a pacemaker, implantable cardioverter defibrillator (ICD) or implantable cardiac monitor, or carried by a medical lead extending from the IMD. One limitation in utilizing implantable acoustical sensors for evaluating heart sounds is the non-cardiac noise that is also sensed by the acoustical sensor and interferes with the detection and processing of heart sounds. Such non-cardiac noise can arise from both physiologic noise sources such as respiration, gastrointestinal, voice, coughing, muscle movement and the like, and non-physiologic noise sources present outside the patient's body.